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## Uses of Package
org.metaqtl

Packages that use org.metaqtl
org.metaqtl |
org.metaqtl.adapter |
org.metaqtl.algo |
org.metaqtl.factory |
org.metaqtl.graph |
org.metaqtl.main |

Classes in org.metaqtl used by org.metaqtl
ChromCluster A cluster of chromosomes which share the same name inside a `MapCluster` framwork.
ChromCluster.ClusterGraph
Chromosome On a Chromosome there are two types of locus : Marker QTL (Quantitative Trait Loci) inside a mapping context which is defined by both the mapping framework (function and unit) and the population cross design used to build this chromosome.
CMarkerSequence A Common marker sequence between two ordered set of markers is a sub-set of at least two markers which order is the same between the two sets (may be reverse).
EMCriteria
EMResult
MetaChrom A MetaChrom is the result of the merge of the members of a `ChromCluster`.
MetaDico This class represents a dictionnary of synonyms.
MetaQtlModel
MetaQtlResult A `MetaQtlResult` is used to store the results of a QTL meta analysis which has been performed for a given trait group on a given chromosome.
MultiFitResult This class represents a result of a multilinear regression analysis.
Qtl A QTL (Quantitative Trait Loci)
Qtl.QTLCross This class stores the informations on the cross design used to detect the QTL.
Qtl.QTLProj This class stores the QTL projection properties.
Qtl.QTLStats This class stores the usual statistics for the QTL.
Qtl.QTLSupport This class stores information on the QTL Confidence Interval
Qtl.QTLTrait This class stores the trait description of a QTL
Tree This class defines a tree.
TreeNode This class represents a node in a binary Tree obtained when applying usual hirarchical clustering methods.

Classes in org.metaqtl used by org.metaqtl.adapter
Chromosome On a Chromosome there are two types of locus : Marker QTL (Quantitative Trait Loci) inside a mapping context which is defined by both the mapping framework (function and unit) and the population cross design used to build this chromosome.
EMResult
MetaMap A `MetaMap` is a bundle of `MetaChrom` objects.
MetaQtlAnalysis A QTL meta analysis consists in a clustering of QTL positions over chromosomes for different group of traits.
MetaQtlData QTL meta analysis first requires to gather the QTL according to the group trait they belong and then to format the QTL data into data points to perfom clustering.
MetaQtlResult A `MetaQtlResult` is used to store the results of a QTL meta analysis which has been performed for a given trait group on a given chromosome.
Qtl A QTL (Quantitative Trait Loci)
QtlPartition

Classes in org.metaqtl used by org.metaqtl.algo
ChromCluster A cluster of chromosomes which share the same name inside a `MapCluster` framwork.
Chromosome On a Chromosome there are two types of locus : Marker QTL (Quantitative Trait Loci) inside a mapping context which is defined by both the mapping framework (function and unit) and the population cross design used to build this chromosome.
CMarkerSequence A Common marker sequence between two ordered set of markers is a sub-set of at least two markers which order is the same between the two sets (may be reverse).
EMResult
IMetaAlgorithm This interface defines some methods which are common to data analysis algorithms.
MetaChrom A MetaChrom is the result of the merge of the members of a `ChromCluster`.
MetaDico This class represents a dictionnary of synonyms.
MetaMap A `MetaMap` is a bundle of `MetaChrom` objects.
MetaQtlAnalysis A QTL meta analysis consists in a clustering of QTL positions over chromosomes for different group of traits.
MetaQtlData QTL meta analysis first requires to gather the QTL according to the group trait they belong and then to format the QTL data into data points to perfom clustering.
MetaQtlResult A `MetaQtlResult` is used to store the results of a QTL meta analysis which has been performed for a given trait group on a given chromosome.
MultiFitResult This class represents a result of a multilinear regression analysis.
Tree This class defines a tree.

Classes in org.metaqtl used by org.metaqtl.factory
EMResult
MetaDico This class represents a dictionnary of synonyms.
MetaMap A `MetaMap` is a bundle of `MetaChrom` objects.
MetaQtlAnalysis A QTL meta analysis consists in a clustering of QTL positions over chromosomes for different group of traits.
MetaQtlModel
Tree This class defines a tree.

Classes in org.metaqtl used by org.metaqtl.graph
Chromosome On a Chromosome there are two types of locus : Marker QTL (Quantitative Trait Loci) inside a mapping context which is defined by both the mapping framework (function and unit) and the population cross design used to build this chromosome.
QtlPartition

Classes in org.metaqtl used by org.metaqtl.main
ChromCluster A cluster of chromosomes which share the same name inside a `MapCluster` framwork.
Chromosome On a Chromosome there are two types of locus : Marker QTL (Quantitative Trait Loci) inside a mapping context which is defined by both the mapping framework (function and unit) and the population cross design used to build this chromosome.
MetaDico This class represents a dictionnary of synonyms.
MetaQtlAnalysis A QTL meta analysis consists in a clustering of QTL positions over chromosomes for different group of traits.
MetaQtlModel
QtlPartition

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